Bioconductor Phylogenetic

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952

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TreeSummarizedExperiment phylogenetic microbiome SummarizedExperiment

updated 2.3 years ago by James W. MacDonald 67k • written 2.3 years ago by Muhammad • 0

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937

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R bioconductor phylogenetic

6.7 years ago cav3gh • 0

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2.1k

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phylogenetic ggtree calibration fossils times-scale

updated 7.3 years ago by Guangchuang Yu ★ 1.2k • written 7.3 years ago by aelgorriaga • 0

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1.5k

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edger differential expression phylogenetic comparative methods

updated 7.5 years ago by Aaron Lun ★ 28k • written 7.5 years ago by noah.reid ▴ 10

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1.2k

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msa phylogenetic

updated 8.0 years ago by UBod ▴ 300 • written 8.1 years ago by vinod.acear ▴ 50

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1.6k

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phylogenetic MacroCAIC

updated 8.9 years ago by Aaron Lun ★ 28k • written 8.9 years ago by Gabi • 0

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1.4k

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linux r phylogenetic computational biology

updated 9.5 years ago by Hervé Pagès 16k • written 9.5 years ago by guilherme • 0

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4.0k

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ape bootstrap node phylogenetic tree

9.5 years ago wd ▴ 30

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7.0k

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ggtree phylogenetic News

updated 9.9 years ago by remi.tournebize ▴ 10 • written 9.9 years ago by Guangchuang Yu ★ 1.2k

9 results • Page 1 of 1

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Replies

Comment: Cross-validation with multiple control subgroups in limma by Ali Barry ▴ 40

Thanks so much for taking the time here, the insights are much appreciated. I suspected I'd have to ad hoc compare results if I did repeat …

Answer: Cross-validation with multiple control subgroups in limma by Gordon Smyth 52k

limma doesn't do cross-validation or resampling. Like most classical linear modeling procedures in statistics, limma uses a statistical mod…

Comment: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio by Robert Castelo ★ 3.4k

Hi Hervé, thank you very much for your input into how to properly build and manage TxDb objects. gDNAx has two main inputs, one or more BAM…

Comment: Biostrings: Error writing long reads (>200 kbps) with writeQualityScaledXStringS by Aidan ▴ 60

Quick update: this is fixed in a branch awaiting PR to Biostrings (https://github.com/Bioconductor/Biostrings/pull/122). Should be in `deve…

Answer: Can DESeq2's design compensate for sequencing experimental design shortcomings? by Michael Love 43k

For statistical analysis plans, I recommend working with a local statistician or someone familiar with linear models in R. I have to reserv…

Votes

C: edgeR and lack of counts ID on CPM matrix

A: DESeq2 Following RSEM

A: importing RSEM data into DESeq2

A: Expected counts from RSEM in DESeq2

A: Using RSEM reads for DESeq2

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